I am looking at Structural Variant analysis with WES data. Is qSV compatible with WES or just WGS? Any other suggestions? Thanks
Due to the exome selection step, structural variant analysis is probably not possible for WES unless you are lucky enough to catch a breakpoint within exon (you can tell if one pair mapped in exon but other pair mapped far away)
Structural variants cannot be captured in exome sequencing? Any alternate methods?
To some degree they can be, as Ying pointed out you may be able to capture some within-gene duplications, deletions, etc. through breakpoint analysis. Those are relatively rare though, and you'd be much more likely to find structural variation within whole genome sequencing data. This is particularly true with larger scale structural variation that may span multiple genes.
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